The Pf3k project is led by researchers at the Broad Institute, the University of Oxford and the Wellcome Trust Sanger Institute.

Our primary goal is to undertake a comprehensive analysis of genome variation in 3,000 parasite samples representing the major malaria endemic regions of the world. In doing so, we'll:

• Provide an open set of P. falciparum genome sequence data that captures common variation across multiple populations in different parts of the world
• Use a combination of short- and long-read sequencing technologies in controlled settings to establish standards for accuracy and completeness in the inference of P. falciparum genome sequence variation and to characterise the quality of information obtained from standard approaches
• Combine information from read-mapping, full de novo assembly, variant assembly and iterative reassembly of specific genes to obtain the most comprehensive resource on P. falciparum variation to date
• Develop new high-quality reference genomes that will increase the resolution and accuracy of variation analysis across the whole sample set
• Analyse the data to learn about parasite population structure, epidemiology and history, mutational and recombinational processes generating diversity, evolutionary processes including drug resistance and immune evasion, and how such phenomena differ between populations and regions

The primary output of the project will be an open access data resource with companion publications on genomic diversity and population genetics that together provide a detailed description of P. falciparum genome variation across the major malaria endemic regions.

Other outputs will include papers on methodology and standardisation of protocols for P. falciparum sequence analysis and genotyping calling. All of the underlying data will be made publicly available for use by the scientific community, initially under Fort Lauderdale conditions.

Scientific working groups will drive forward specific areas of analysis including statistics and population genetics (led by Gil McVean and Roberto Amato), technology benchmarking (led by Dan Neafsey and Jim Stalker) and reference genomes (led by Matt Berriman and Thomas Otto).  The MalariaGEN Resource Centre will provide support for partner studies, data production pipelines, communications and project management. The Project is overseen by the Pf3k Management Committee that is comprised of working group leaders, with support from members of the MalariaGEN Resource Centre.